{"id":"W2169882791","doi":"10.1016/j.gene.2004.12.011","title":"Site interdependence attributed to tertiary structure in amino acid sequence evolution","year":2005,"lang":"en","type":"article","venue":"Gene","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":104,"is_retracted":false,"has_abstract":false,"ca_institutions":"McGill University; Canadian Institute for Advanced Research; Université de Montréal","funders":"Université de Montréal; Canada Research Chairs; Génome Québec","keywords":"Biology; Pairwise comparison; Phylogenetic tree; Sequence (biology); Threading (protein sequence); Context (archaeology); Multiple sequence alignment; Alignment-free sequence analysis; Tree (set theory); Computational biology; Sequence alignment; Phylogenetics; Set (abstract data type); Molecular evolution; Protein tertiary structure; Evolutionary biology; Peptide sequence; Computer science; Genetics; Protein structure; Mathematics; Artificial intelligence; Combinatorics; Paleontology; Gene","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0007840534,0.0002415721,0.0004171205,0.0008669515,0.0004648148,0.0007025325,0.0003795559,0.0004249436,0.001918089],"category_scores_gemma":[0.001362048,0.0003051088,0.0003382823,0.0008081429,0.0005409032,0.0009034352,0.0004374643,0.0007074023,0.0004425348],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002857638,"about_ca_system_score_gemma":0.0002096355,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001915071,"about_ca_topic_score_gemma":0.0003752123,"domain_scores_codex":[0.9996566,0.0001075932,0.00002679068,0.00009044347,0.00007983861,0.00003877462],"domain_scores_gemma":[0.997228,0.001321475,0.0004671174,0.0004909412,0.0002853518,0.0002072044],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0007615603,0.0001496712,0.04000086,0.0001727588,0.00008438338,0.0004172779,0.0002976079,0.002729254,0.9324513,0.005743454,0.00009578856,0.01709606],"study_design_scores_gemma":[0.00006188515,0.0007416773,0.5839016,0.00008099621,0.0004216831,0.00273713,0.0003611609,0.03857562,0.3554391,0.01349912,0.004109698,0.00007030988],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9924232,0.0003966169,0.004766753,0.00003762171,0.00001036027,0.00001099949,0.00005944175,0.00003785214,0.002257121],"genre_scores_gemma":[0.9973831,0.0002325972,0.001614138,0.00003447162,0.00002213019,0.000009553208,0.000149088,0.00002616929,0.0005286997],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001918089,"threshold_uncertainty_score":0.006416619,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009726490430959822,"score_gpt":0.2389632307348782,"score_spread":0.2292367403039183,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}